Existing methods for DNA-based profiling have drawbacks which compromise their accuracy, efficiency, ease of use, and scalability. For example, DNA profiling methods such as karyotyping and fluorescent in situ hybridization (FISH) are time consuming and technically demanding. DNA microarray hybridization technologies, such as comparative genome hybridization (CGH) and Representational Oligonucleotide Microarray Analysis (ROMA), are similarly time consuming, require large amounts of input DNA material, and a considerable expenditure in specialized equipment. These and other drawbacks prevent the widespread adoption of genetic profiling methods for clinical use.
Real-time quantitative, polymerase chain reaction techniques (QPCR) are accepted as a gold standard for quantitative analysis of DNA. However, such techniques have generally only been applied to analyze a small number of target DNA sequences because of the lack of an analytical algorithm with sufficient statistical power to provide reliable data for a robust set of target DNA sequences of interest.
Thus, a need exists for efficient, easy to use, rapid, accurate, and scalable systems and methods for DNA-based profiling that can be used in, for example, clinical use for diagnosis and/or evaluation. It is desirable that the systems and methods supplant less sensitive, hybridization based methodologies and provide the high sensitivity achieved with QPCR methods. It is also desirable that the systems and methods overcome the analytical limitations encumbered by conventional computational methods typically confounding QPCR analyses. It is also desirable that the systems and methods be customizable to a diverse set of applications or customizable for individual patients. It is also desirable that the systems and methods only require readily attainable and small amounts of input samples. Finally, it is desirable that the systems and methods are capable of identifying, for each application area of interest, the appropriate target DNA sequences that are most relevant for DNA-based analysis for that application.